The Psychic Jinjuuriki Retold
by adrogoz
Summary: Re-write from the beginning. When Mewtwo finds himself in another world with no memory of how he got there, he trains a young outcast from a ninja village in order to regain his memories and return home. But they may find themselves uncovering in a larger plot, stretching across an entire multiverse
1. Chapter Hoopa

Groaning and struggling with a painful headache, Mewtwo awoke in an unfamiliar forest. He wasn't sure how long he had been unconscious... or where he was, for that matter. _Did I teleport there?_ he wondered, trying to remember how and why he came to this place. Much to his surprise, he couldn't remember. _Amnesia maybe? The effects should have ended by now. Strange._

Closing his eyes, he attempted to teleport himself back to his lair in Cerulean Cave, but nothing happened. Blaming it on his confused state, Mewtwo focused and tried again, for no result.

 _How unusual,_ the genetic experiment mused, as he observed his surroundings in search for an explanation. From the looks of the weapons he could see stabbed into some of the trees, this area was either the site of a small battle or a training ground. _Maybe the local humans do not have many Pokémon to fight for them? To rely on weapons, they must be helpless on their own. Did I fought them and used Amnesia to increase my chances of winning?_ He shrugged. _As if humans could fight me._

The experimental Pokémon decided to investigate the area, and eventually found the entrance to some kind of town or village. It had unusually high walls for a settlement of its size, and lacking in buildings. _It looks like a fortress. Did I teleported to a primitive land, far away from Kanto?_

Normally, having little interest in humans and no desire to be captured by trainers or to cross Team Rocket's path ever again, Mewtwo avoided cities and human settlements. Today, he would make an exception. Visiting this town could refresh his memory, or at least give him an vague idea where he was. Using a cloak he stole from some shop to hide his features, Mewtwo discreetly used his powers to mentally block people's suspicions. Even with a cloak, he was quite unusual, and he had to avoid questions. To everyone, he was simply a normal human nothing short of average.

Walking around the city, Mewtwo was surprised to see no Pokémon accompanying the people walking around in the town, and no belts of Pokéballs. Many of them wore headbands with a symbol on them resembling a spiral with a point at the bottom-right corner. Scanning people's mind with telepathy provided some answers. Firstly, the town was called Konoha, located on a continent he couldn't picture himself. He had already seen world maps, and no landmass matched the people's thoughts.

Secondly, they didn't have Pokémon because _they didn't even know what they were_.

 _Either I am dreaming, or in another world. Is someone using Dream Eater on me?_

"Stay away from that boy. He's nothing but trouble."

His thoughts were suddenly disrupted when he heard a woman whispering something strange to her two children. A boy of about seven or eight with spiky blonde hair and unusual marks resembling whiskers on his cheeks passed the other way, sighed sadly, and continued walking.

Intrigued, Mewtwo used his psychic powers to delve into the boy's mind. The kid had to have done something to deserve such treatment, and he was curious what. He was immediately startled upon realizing there were two minds within this child. _I thought only a Dodrio or a Magneton had that problem? Is he possessed by a Ghost-Type?_ he wondered.

After a closer telepathic examination, he realized only one mind belonged to the boy. He was an orphan, Naruto Uzumaki, and for some reason nearly everyone he had met seemed to deliberately ignore or mistreat him. The Hokage, the village's leader, had given him an apartment and a place in some sort of academy, but other than that, nearly everyone else treated him as if he was some kind of criminal, and the boy had no idea why.

He wanted to be the Hokage so everyone would have to respect him and look up to him.

Shaking his head in a mix of pity and sadness, the mind reader attempted to dwelve into the second mind next, which proved to be a far more difficult task. _Either a Psychic or a Ghost,_ Mewtwo decided, persisting, _no one else could-_

Mewtwo suddenly found himself in a vast room, where the floor was flooded. One wall was replaced with a vast caged door, with a seal on its center. Inside the cage? The biggest Ninetails he had ever seen. Even bigger than a Wailord, and obviously more ferocious than even Rayquaza. The fur was orange, however, and it didn't have the psychic feel of Fire-Types. In fact, Mewtwo had no idea which type it was.

The mind reader suddenly realized it wasn't a Ninetails... the creature simply had the appearance of one.

"What are you?" Mewtwo asked, more to himself than the beast.

"I could ask you the very same question," the fake Ninetails replied, sounding both intrigued and annoyed. "I have never seen your kind before, and it appears that you are far more powerful than any of those disgusting humans. A new specie? Or maybe mankind once again screwed up and tried to play gods?"

"My name is Mewtwo," the Genetic Pokémon spoke, disturbed by the monster's insight. Was it another experiment? Anyway, the sheer malice emanating from the thing didn't mesh well with the Psychic. Whatever the monster was, it was obviously malevolent. "And that is all you need to know".

The beast behind the bars laughed, a red glow emanating out from its eyes. The monster's bloodlust gave Mewtwo the chills.

"A pleasure to meet you, Mewtwo. I have the feeling we will meet again... and I will enjoy devouring you whole."

Suddenly, the monster's killing intent skyrocketed, triggering a flashback. The Psychic was in his cave, fighting against two other Pokémon. The first was Moltres, a golden birdlike creature with a flaming crest and wings, and its partner a black and silver being with seven red eyes... Registeel.

Back in the street, Mewtwo groaned. He needed to somehow gather more of that creature's energy in order to remember more, he was sure of it. But how? A Masterball? No, he wasn't that sadistic. And he had the feeling this blonde was a human Pokéball on his own. _Must be why everyone keep their distance with him,_ Mewtwo realized, _these people must hate this beast. Seeing its malevolence, I can guess why._

... the boy. The boy was the key.

"Your name is Naruto, right?" he asked the boy.

"Who, me?", said the boy, looking somewhat surprised. Since nobody safe the Hokage and the owners of a restaurant ever talked to him without insults, Mewtwo could understand his reaction. He even looked eager. "I'm Naruto Uzumaki. Who are you?"

"That is not important", said Mewtwo. "I have an offer for you".

"An offer?" Naruto asked. "What kind of offer?"

"You would be my student", Mewtwo explained. If he could keep a being of such evil contained, he _had_ to have some psychic abilities. Developing his potential might be the key to understand his situation. Beside, he had nothing else to do, and he knew what it was to be alone and feared at birth.

Mewtwo had seen a kindred spirit, and even if he had some reluctance, he felt compelled to lend the boy a hand.

"I could teach you techniques this world has never seen before. Enough to command the respect of your classmates, no doubt." _Hook, line and sinker._

Naruto's eyes lit up. "Really?" he asked with eagerness.

"Meet me at..." he scanned the boy's mind, finding the name of his favorite restaurant. "Ichiraku ramen, after your classes tomorrow... if you accept my offer", said Mewtwo, before teleporting away.

Obviously, if seeing _that_ couldn't convince the boy, then Mewtwo didn't know what to do.

* * *

The next day, Naruto arrived at Ichiraku as the cloaked stranger had instructed, and a few minutes later, by which time Naruto had already eaten two bowls of ramen, the stranger suddenly materialized... right next to the blonde.

He _had_ to learn that. That would be _so_ cool.

"You're late," Naruto couldn't help but say, immediately regretting his words. _It's the only guy willing to teach me, don't screw it up you idiot!_

"I left enough time so that you could have your meal," the stranger shrugged, before placing a hand on Naruto's shoulder.

The next second, they had left Ichiraku for an unusual room with various bizarre machines stacked all around them.

"So, are you ready to begin training? I'm not going to be soft on you."

"I sure am! Believe it!" Naruto answered enthusiastically, before suddenly realizing the guy had a tail. And grey skin.

The stranger dropped the cloak to reveal the most bizarre creature Naruto had ever seen. He was a light grayish humanoid, with a _long_ purple tail. He had three fingers on each hand, two toes on each foot and two freaky ears. A cord ran out from the back of his head into his back.

"Wh-what are you?" asked Naruto in surprise.

"My name," the creature locked eyes with him, "is Mewtwo"

 _ **Adrogoz' Notes:**_ _ **I feel this first chapter, having already been rewritten (by me and others) is fine as-is. Bit of a cheat for a rewrite, but the coming chapters will be improved**_


	2. Chapter Wigglytuff

From that point on, Naruto went to train with Mewtwo after class every day. After figuring out how to channel chakra to the brain to unlock one's psychic potential, Mewtwo taught Naruto a multitude of techniques known in his world. Psychic techniques were his specialty, from "basic" mind-reading to a variety of attacks.

Not wanting him to over-specialize, Mewtwo also taught Naruto some physical techniques and cover what he could from other types. Apparently some of them were near-impossible to chakra-using humans (Mewtwo was surprised to learn most Grass and Ice-type attacks were only possible for a few extinct bloodlines), but he taught what he could. Of course, seeing how most of the village already hated Naruto, Mewtwo insisted he "play down" his psychic abilities so as not to rouse any fear or suspicion. There were a few close scrapes, but nothing Mewtwo couldn't fix with a quick memory wipe...

Mewtwo initially only used the training as a means of using the Nine tailed Fox's chakra to unblock his memories, and on that front he made some slow progress (apparently just before he had awoken in the Hidden Leaf, he had been targeted by a trainer who had already captured several Legendary Pokemon, how this had lead to him ending up in another dimension though...) However, it wasn't long before he actually saw Naruto as his student, rather than a tool to find out what had happened to him and how he had gotten stuck in this world.

 _Not like my own world ever accepted me anyway..._

* * *

It was now five years since Naruto started training with Mewtwo. Naruto had just graduated from the ninja academy. He had actually failed the final test (unfortunately, nothing Mewtwo taught him was on the test.. .) , but one of his teachers, Mizuki, had approached him after school about a supposed secret method of graduating involving taking a scroll from a top-secret vault and learning a jutsu  
from it. He clearly didn't know Naruto could read his mind (a technique Mewtwo had taught him) and when Naruto refused, Mizuki had attempted to steal the scroll himself. By this time, Naruto had informed Iruka of Mizuki's plans and they stopped him in his tracks. Naruto's Psycho Cut attack had even impressed Iruka enough for him to allow Naruto to graduate.

* * *

And now he was in class, waiting to hear who he would be on the same squad as.

"Naruto? What are you doing here?" asked a voice as Naruto entered the classroom. It was Kiba, one of Naruto's classmates.  
"Only people who graduated are supposed to be here now", added Ino, another classmate.  
"I did graduate", said Naruto. "See the headband?"  
Naruto sat down, but was immediately pushed aside by Sakura, who wanted to sit beside Sasuke, the most popular boy in the class. Despite this, he seemed to do nothing but brood and ignore the fangirls.  
"Hope I'm not in a team with him", muttered Naruto to himself.  
"Squad 7", announced Iruka. "Naruto Uzumaki, Hinata Hyuga and Sasuke Uchiha".  
Naruto groaned. Sasuke was the one he least wanted to be in a squad with, and he barely knew Hinata, owing to the fact that she always went quiet when he was around for some bizarre reason. He had asked Mewtwo about it, but the Psychic Pokémon had always ignored those questions.  
 _So I'm not with Sasuke,_ thought Sakura _. At least Ino-pig isn't either_  
"So Sasuke is in the same squad as the one girl who isn't crazy about him", said Shikamaru. "How ironic".  
"Squad 8", continued Iruka. "Shino Aburame, Sakura Haruno, Kiba Inuzuka".  
Sakura looked at her teammates with indifference, still disappointed she wasn't in the same team as Sasuke, while Ino made some remark about how she would hate to be in a team with Shikamaru.  
"Squad 10", announced Iruka. "Shikamaru Nara, Choji Akamichi, Ino Yamanaka".  
"You were saying?" said Shikamaru.

* * *

After that, the class was told to have a break for an hour before meeting their respective sensei. Naruto opted to use this time to fill in Mewtwo about his team.  
"From the sound of things, you dislike the Uchiha boy", said Mewtwo.  
"Yeah, Hinata's all right I guess", said Naruto. "At least I didn't get stuck with one of the Sasuke fangirls".  
"An Uchiha and a Hyuga", said Mewtwo, more to himself than to Naruto. "Perhaps they thought your mind-reading was some form of Dojutsu, so it seems likely they made this team as a full squad of ninjas with ocular bloodlines".  
"That sounds cool", said Naruto. "But I don't have any eye powers".  
"That shouldn't be a problem", said Mewtwo. "Just try not to give the impression that you're a fool".

 ** _I split this chapter in two for the rewrite, it was probably the most rushed bit in the whole story. This part, I think, hints at some slight changes I'll be making to this rewrite and also fixes a few odd pseudo-plotholes of the original. Anyway…_**

 ** _New Instruments coming sort of soon!_**


End file.
